The typical Boeing Systems Engineer salary is $84,476. Systems Engineer salaries at Boeing can range from $65,000 - $119,841. This estimate is based upon 20 Boeing Systems Engineer salary report(s) provided by employees or estimated based upon statistical methods. When factoring in bonuses and additional compensation, a Systems Engineer at Boeing can expect to make an average total pay of $86,112 . See all Systems Engineer salaries to learn how this stacks up in the market.